From c294136b0b9f66f8b9cae00c3f2c922d1cee52ac Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Tue, 28 Mar 2023 12:32:22 -0400 Subject: [PATCH 1/3] Replaced original_knowledge_source with primary_knowledge_source. As per #628. --- .../scala/org/renci/cam/QueryService.scala | 36 +++++++++---------- 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/src/main/scala/org/renci/cam/QueryService.scala b/src/main/scala/org/renci/cam/QueryService.scala index cd8becfc..e481250d 100644 --- a/src/main/scala/org/renci/cam/QueryService.scala +++ b/src/main/scala/org/renci/cam/QueryService.scala @@ -6,14 +6,14 @@ import io.circe.syntax._ import org.apache.jena.query.QuerySolution import org.apache.jena.rdf.model.Resource import org.phenoscape.sparql.SPARQLInterpolation._ -import org.renci.cam.Biolink.{BiolinkData, biolinkData} +import org.renci.cam.Biolink.{biolinkData, BiolinkData} import org.renci.cam.HttpClient.HttpClient import org.renci.cam.SPARQLQueryExecutor.SPARQLCache import org.renci.cam.Util.IterableSPARQLOps import org.renci.cam.domain.PredicateMappings.{getBiolinkQualifiedPredicates, mapQueryEdgePredicates} import org.renci.cam.domain._ -import zio.config.{ZConfig, getConfig} -import zio.{Has, RIO, Task, UIO, ZIO, config => _} +import zio.config.{getConfig, ZConfig} +import zio.{config => _, Has, RIO, Task, UIO, ZIO} import java.math.BigInteger import java.nio.charset.StandardCharsets @@ -200,8 +200,8 @@ object QueryService extends LazyLogging { // Generate the attributes we will need to produce the edge output. originalKS <- ZIO - .fromOption(biolinkData.predicates.find(p => p.shorthand == "original_knowledge_source")) - .orElseFail(new Exception("could not get biolink:original_knowledge_source")) + .fromOption(biolinkData.predicates.find(p => p.shorthand == "primary_knowledge_source")) + .orElseFail(new Exception("could not get biolink:primary_knowledge_source")) aggregatorKS <- ZIO .fromOption(biolinkData.predicates.find(p => p.shorthand == "aggregator_knowledge_source")) .orElseFail(new Exception("could not get biolink:aggregator_knowledge_source")) @@ -674,9 +674,9 @@ object QueryService extends LazyLogging { predicate = querySolution.getResource(queryEdgeID).getURI predicateIRI = IRI(predicate) tripleString = TripleString(source, predicate, target) - originalKS <- ZIO - .fromOption(biolinkData.predicates.find(p => p.shorthand == "original_knowledge_source")) - .orElseFail(new Exception("could not get biolink:original_knowledge_source")) + primaryKS <- ZIO + .fromOption(biolinkData.predicates.find(p => p.shorthand == "primary_knowledge_source")) + .orElseFail(new Exception("could not get biolink:primary_knowledge_source")) aggregatorKS <- ZIO .fromOption(biolinkData.predicates.find(p => p.shorthand == "aggregator_knowledge_source")) .orElseFail(new Exception("could not get biolink:aggregator_knowledge_source")) @@ -693,19 +693,19 @@ object QueryService extends LazyLogging { Some(appConfig.location), None, None) - originalKSstr = provValue match { + primaryKSstr = provValue match { case ctd if provValue.contains("ctdbase.org") => "infores:ctd" case _ => "infores:go-cam" } - originalKSAttribute = TRAPIAttribute(Some("infores:cam-kp"), - originalKS.iri, - None, - List(originalKSstr), - Some(infoResBiolinkClass.iri), - Some(provValue), - None, - None) - attributes = List(aggregatorKSAttribute, originalKSAttribute) + primaryKSAttribute = TRAPIAttribute(Some("infores:cam-kp"), + primaryKS.iri, + None, + List(primaryKSstr), + Some(infoResBiolinkClass.iri), + Some(provValue), + None, + None) + attributes = List(aggregatorKSAttribute, primaryKSAttribute) relationLabelAndBiolinkPredicate <- ZIO .fromOption(relationsMap.get(predicateIRI)) .orElseFail(new Exception("Unexpected edge relation")) From 226ecfc22ee2f87d9ae10f04e29a22162708b229 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Fri, 31 Mar 2023 16:44:45 -0400 Subject: [PATCH 2/3] Replaced originalKS with primaryKS for clarity. --- src/main/scala/org/renci/cam/QueryService.scala | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/main/scala/org/renci/cam/QueryService.scala b/src/main/scala/org/renci/cam/QueryService.scala index e481250d..8ef405c8 100644 --- a/src/main/scala/org/renci/cam/QueryService.scala +++ b/src/main/scala/org/renci/cam/QueryService.scala @@ -6,14 +6,14 @@ import io.circe.syntax._ import org.apache.jena.query.QuerySolution import org.apache.jena.rdf.model.Resource import org.phenoscape.sparql.SPARQLInterpolation._ -import org.renci.cam.Biolink.{biolinkData, BiolinkData} +import org.renci.cam.Biolink.{BiolinkData, biolinkData} import org.renci.cam.HttpClient.HttpClient import org.renci.cam.SPARQLQueryExecutor.SPARQLCache import org.renci.cam.Util.IterableSPARQLOps import org.renci.cam.domain.PredicateMappings.{getBiolinkQualifiedPredicates, mapQueryEdgePredicates} import org.renci.cam.domain._ -import zio.config.{getConfig, ZConfig} -import zio.{config => _, Has, RIO, Task, UIO, ZIO} +import zio.config.{ZConfig, getConfig} +import zio.{Has, RIO, Task, UIO, ZIO, config => _} import java.math.BigInteger import java.nio.charset.StandardCharsets @@ -199,7 +199,7 @@ object QueryService extends LazyLogging { appConfig <- getConfig[AppConfig] // Generate the attributes we will need to produce the edge output. - originalKS <- ZIO + primaryKS <- ZIO .fromOption(biolinkData.predicates.find(p => p.shorthand == "primary_knowledge_source")) .orElseFail(new Exception("could not get biolink:primary_knowledge_source")) aggregatorKS <- ZIO @@ -237,7 +237,7 @@ object QueryService extends LazyLogging { } originalKSAttributes = originalKnowledgeSources.map { case (derivedFrom, inforesKS) => TRAPIAttribute(Some("infores:cam-kp"), - originalKS.iri, + primaryKS.iri, None, List(inforesKS), Some(infoResBiolinkClass.iri), From faadb31c59888f2e3b19c177e16a7a0a3aadd3e2 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Fri, 31 Mar 2023 17:16:25 -0400 Subject: [PATCH 3/3] Incremented version to 0.3 for release. --- build.sbt | 2 +- src/main/resources/application.conf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/build.sbt b/build.sbt index a5423a92..3a2b8bde 100644 --- a/build.sbt +++ b/build.sbt @@ -8,7 +8,7 @@ organization := "org.renci" name := "cam-kp-api" -version := "0.3-pre4" +version := "0.3" licenses := Seq("MIT license" -> url("https://opensource.org/licenses/MIT")) diff --git a/src/main/resources/application.conf b/src/main/resources/application.conf index 893da615..f86f8adb 100644 --- a/src/main/resources/application.conf +++ b/src/main/resources/application.conf @@ -1,5 +1,5 @@ { - version = "0.3-pre4" + version = "0.3" host = 0.0.0.0 port = 8080 port = ${?PORT}